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This article discusses two main topics. The first topic is a study that found excessive use of four laboratory tests: HbA1c, PSA, vitamin D, and lipid panel tests. The authors suggest reducing unnecessary testing and using the savings to test undertested areas and fund unreimbursed tests. The second topic is the use of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases. The study found that mNGS testing accurately detected pathogens in body fluid samples, even when routine testing was negative. The article concludes that mNGS testing has the potential to improve diagnostic accuracy and streamline testing processes in clinical laboratories. Additionally, a separate study estimated that excessive testing cost over $350 million in 2019 and emphasizes the need to address unnecessary testing to redirect resources for greater patient benefit. [Extracted from the article]

suggest that telomere shortening may be a potential biomarker for assessing the severity and prognosis of AUD, and that interventions targeting telomere maintenance may be beneficial for these patients. [Extracted from the article]

The article informs about Eukaryogenesis, which is broadly defined as the evolutionary path taken by increasingly complex lifeforms as they diverged from the prokaryotes that dominated the early part of Earth's biological history. Topics include functional period of eukaryogenesis started just prior to the symbiosis between two prokaryotes and modern eukaryotes arose; and identity of original host in the symbiotic partnership and processes associated with modern eukaryotic cells evolved.

Researchers at the University of Hong Kong conducted a study to investigate the role of gut microbiota in the immune response following three doses of the BNT162b2 COVID-19 vaccine. They found that certain bacterial species, such as Streptococcus parasanguinis and Bacteroides stercoris, were associated with a lower immune response at one year, while others like Bifidobacterium pseudocatenulatum and Clostridium leptum were associated with a better response. These findings suggest that the baseline gut microbiota may play a role in long-term immune response to the vaccine. Further research is needed to better understand this relationship. [Extracted from the article]

A study conducted by researchers at the First Affiliated Hospital of Zhengzhou University in China compared the clinical performance of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) for detecting microorganisms in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). The study found that both mNGS and tNGS had higher positive rates and sensitivity compared to conventional microbiological tests (CMT) for overall, bacterial, and fungal detection. However, mNGS outperformed tNGS in terms of sensitivity and true positive rate, particularly for bacteria and viruses. The study also observed that the detection of Torque teno virus (TTV) decreased as the post-transplantation time increased. Overall, both mNGS and tNGS were found to be superior to CMT in identifying respiratory pathogens among KTRs. [Extracted from the article]

The article discusses a case study where metagenomics sequencing was used to investigate the role of oral bacteria in dementia. Topics include: the use of 16S metagenomics sequencing to detect bacterial DNA, the identification of Spirochaetes phylum in the patient's microbiome, and the potential link between oral infections and neurodegenerative conditions.

The article reports on a study from Shulan (Hangzhou) Hospital evaluating the use of metagenomic next-generation sequencing (mNGS) for early detection of infections post-liver transplantation. Topics include the comparative effectiveness of mNGS versus culture methods in identifying pathogens, the role of mNGS in predicting infection outcomes and patient survival, and the use of inflammatory biomarkers and real-time PCR in monitoring infections and patient prognosis.

The article reports on a patent application for a novel 2-gene host-viral transcriptomic classifier aimed at improving COVID-19 diagnostics. Topics discussed include the development of this classifier through upper respiratory transcriptional profiling, its integration with existing polymerase chain reaction (PCR) platforms for enhanced detection, and the potential for reduced false positives and negatives compared to traditional methods.

The article from the University of Eastern Finland explores advancements in understanding atrial fibrillation (AF) through various omics approaches. Topics discussed include the role of genetics and transcriptomics in identifying AF risk factors, the contributions of metabolomics and metagenomics in understanding AF pathogenesis, and the need for further validation of these findings to improve diagnostics and treatment.

A patent application has been submitted for a method of detecting secondary infections in patients with a primary infection, such as COVID-19. The method involves analyzing plasma samples for microbial cell-free nucleic acids (mcfNA) from different microbes using next-generation sequencing. By comparing the amount of mcfNA to a threshold, secondary infections can be detected. This method could help improve the diagnosis and treatment of secondary infections in patients with severe pneumonia or acute respiratory distress syndrome. [Extracted from the article]

A study conducted at Zhengzhou University People's Hospital in China explored the clinical utility of metagenomic next-generation sequencing (mNGS) in diagnosing invasive pulmonary aspergillosis (IPA) in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) in the intensive care unit (ICU). The study found that mNGS had a higher sensitivity in diagnosing IPA compared to fungal culture and galactomannan (GM) testing. Combining mNGS with conventional methods resulted in a higher diagnostic rate for IPA. The researchers concluded that mNGS could be a valuable complementary tool for diagnosing IPA in AECOPD patients. [Extracted from the article]

A recent study aimed to investigate the relationship between the gut microbiome and serum levels of uremic molecules in adults undergoing hemodialysis. The study found that there were no differences in the gut microbiome associated with uremic toxin levels. Instead, the relative availability of dietary protein and fiber was significantly associated with uremia. The study suggests that hemodialysis patients have sufficient microbial enzymatic capacity for the synthesis of these molecules, and that the primary driver of production is the availability of protein versus fiber. However, it is important to note that this study has not yet undergone peer review. [Extracted from the article]

A recent study conducted at the First Affiliated Hospital of Dalian Medical University in China highlights the importance of early diagnosis and treatment for rhino-orbital-cerebral mucormycosis (ROCM), a rare and potentially fatal fungal infection. The researchers presented a case of a 46-year-old man with diabetes who experienced vision loss, swelling, and headaches that rapidly worsened and led to death. The infection was confirmed as a fungal Rhizopus arrhizus infection using metagenomics next-generation sequencing (mNGS). The study suggests that mNGS testing should be strongly recommended for highly suspected patients. [Extracted from the article]

A recent study conducted by researchers at the Fifth Affiliated Hospital of Sun Yat-Sen University explores the interplay between the microbiota and host in early-stage lung adenocarcinoma (ES-LUAD) among non-smokers. The study found that patients with ES-LUAD exhibited local microbial dysbiosis, suggesting the potential pathogenicity of certain microbial species. Through multi-omics correlations, the researchers observed intricate local crosstalk between the host and local microbial communities. Additionally, a diagnostic model composed of six bacterial markers was developed, which successfully differentiated between patients with ES-LUAD and healthy controls. This study enhances our understanding of the pathogenic mechanisms underlying ES-LUAD and provides a potential diagnostic tool for distinguishing between ES-LUAD and healthy individuals. [Extracted from the article]

Researchers from the Federal University of Minas Gerais in Brazil have conducted a study using nanopore metagenomics to identify microorganisms associated with acute febrile illness (AFI) and severe neurological disorders (SNDs) of unknown origin. The study involved analyzing samples from fourteen hospitalized patients and identified a range of disease-associated microbes, including Escherichia coli, Streptococcus sp., Human Immunodeficiency Virus 1, Human Pegivirus, Clostridium sp., and Dengue virus type 2. The findings demonstrate the efficiency and adaptability of metagenomic analysis in pathogen identification and offer promising prospects for advancing our understanding and control of infectious diseases. [Extracted from the article]

A recent study conducted at Peking University People's Hospital in Beijing, China, explored the clinical impact of plasma metagenomic next-generation sequencing (mNGS) on infection diagnosis and antimicrobial therapy in immunocompromised patients. The study found that mNGS significantly improved the diagnostic rates for fungal infections in patients with neutropenia and non-neutropenia, compared to patients with non-hematologic diseases. The use of mNGS also had positive impacts on therapy, outweighing any negative impacts. The study concluded that plasma mNGS has a clinically confirmed positive impact on the diagnosis of fungal infections and antimicrobial therapy in immunocompromised patients. [Extracted from the article]

A recent study conducted at the University of Dhaka in Bangladesh explored the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility. The study found that infertile women had a bacterial community primarily composed of Lactobacillus, Gardnerella, and Prevotella, while fertile women exhibited a more diverse composition with reduced abundance of Lactobacillus and Gardnerella. The study suggests that lower species diversity with a higher abundance of Lactobacillus iners, Lactobacillus gasseri, and Gardnerella vaginalis may contribute to female infertility. However, larger sample sizes are needed to further evaluate this association. [Extracted from the article]

A recent study conducted at Zhuhai People's Hospital in China explored the role of gut microbiota in acute coronary syndrome (ACS), a leading cause of mortality. The researchers sequenced the gut microbiota of 38 ACS patients before and after treatment, and observed changes in the abundance of certain bacterial species and metabolic pathways. They found that different statins used in therapy had varying effects on the gut microbiota. The study provides valuable insights into ACS and may contribute to improved diagnosis and therapy for patients. [Extracted from the article]

A study conducted at Shenzhen Second People's Hospital in China investigated the use of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in diagnosing and treating intracranial infections. The study compared the detection rates and reporting times of CSF mNGS and conventional microbial culture methods. The results showed that CSF mNGS had a higher pathogen detection rate and faster reporting time compared to microbial culture. The application of CSF mNGS was found to improve the detection rate of intracranial infection pathogens, potentially leading to shorter antibiotic use and reduced intensity of broad-spectrum antibiotics. [Extracted from the article]

A preprint abstract from biorxiv.org discusses the response of soil microbes to multiple global change (GC) factors. The study applied 10 GC treatments individually and in random combinations to soil samples and monitored their bacterial and viral composition using metagenomic analysis. The results showed that the application of multiple GC factors selected for specific prokaryotic and viral communities, favoring potentially pathogenic unknown mycobacteria and novel viruses. Additionally, the study found that multiple GC factors selected for bacteria with diverse metabolic capabilities and a high load of antibiotic resistance genes. The research suggests that multiple GC factors impose selective pressures on soil microbes that are not observed at the individual factor level, providing insights into how GC interactions shape microbial communities. [Extracted from the article]

A recent study conducted in Cosseys Reservoir, New Zealand, examined the impact of short-term warming on freshwater ecosystems. The researchers found that even modest temperature increases of 2-5 degrees Celsius can lead to an increase in harmful cyanobacterial blooms and antibiotic resistance. The study also revealed that reactive oxygen species (ROS) stress intensified the proliferation of antibiotic resistance genes. These findings highlight the complex challenges posed by climate change to water quality and public health. However, it is important to note that this study has not yet undergone peer review. [Extracted from the article]

Researchers at Peking University People's Hospital in Beijing, China have published a case report on the use of metagenomic next-generation sequencing (mNGS) for the timely diagnosis of a traveler with nonspecific febrile Q fever. Q fever is a global disease caused by the bacterium Coxiella burnetii. The patient in this case experienced a persistent fever accompanied by other symptoms, and while traditional tests were negative, mNGS detected the presence of C. burnetii in the patient's blood. The researchers concluded that mNGS can provide an early and timely diagnostic tool for difficult-to-culture pathogens, contributing to successful clinical treatment. [Extracted from the article]

A recent study conducted at Peking Union Medical College Hospital aimed to investigate the diagnostic performance of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and chromosome copy number variations (CNVs) analysis in the detection of leptomeningeal malignancy. The study included 51 patients, with 34 diagnosed with leptomeningeal malignancies and 17 diagnosed with central nervous system (CNS) inflammatory diseases. The results showed that CSF mNGS-CNVs had higher specificity compared to traditional cytology and can be used as a complementary diagnostic method for patients with leptomeningeal malignancies. The study was funded by the National High Level Hospital Clinical Research Funding. [Extracted from the article]

The article discusses the challenge of identifying and understanding novel genes from microbiomes. The authors propose a method called METa assembly, which allows for the creation of functional metagenomic libraries using smaller amounts of DNA. They demonstrate that this method can be used to link certain genes to antibiotic resistance and potential resistance to the antidiabetic drug acarbose. The study suggests that METa assembly can overcome the limitation of requiring large amounts of DNA and expand the possibilities for functional metagenomic research. [Extracted from the article]

A study conducted at Can Tho University in Vietnam has explored the use of clustering algorithms and deep learning techniques to analyze complex metagenomic data for personalized medicine. The researchers utilized clustering algorithms such as DBSCAN, BIRCH, and OPTICS to identify patterns in the data and generate visualizations. They also integrated a shallow convolutional neural network for disease prediction tasks. The study found that BIRCH performed well in diagnosing Type 2 diabetes, while DBSCAN was effective in diagnosing Colorectal cancer and Inflammatory Bowel Disease. This research has been peer-reviewed and provides valuable insights into the application of machine learning in personalized medicine. [Extracted from the article]

A recent study conducted a global survey of the gut bacterium Ruminococcus gnavus and found that it is highly prevalent in Westernized populations and in newborns and infants. The study also discovered multiple clades within R. gnavus that separate isolates from healthy individuals and those with Crohn's disease. Functional analyses of genes did not explain this separation, but bacterial GWAS revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and putative mucin foraging. This study provides valuable insights into the global distribution and genomic variation of R. gnavus. [Extracted from the article]

A recent report from Nitte (Deemed to be University) highlights the prevalence and impact of oral squamous cell carcinoma (OSCC), which is the 14th most common cancer worldwide. The study focused on the role of the oral microbiome in OSCC and found distinct microbial signatures in tumor tissues compared to non-cancerous tissues. The researchers identified specific bacteria, such as Fusobacterium, Prevotella, and Bacteroidetes, that were significantly enriched in OSCC lesions. Additionally, the study revealed metabolic pathways associated with these microbes that may contribute to OSCC pathogenesis. While the microbial signatures are important, the researchers also emphasized the influence of host factors and the oral microenvironment on OSCC development. [Extracted from the article]

Researchers from the First Affiliated Hospital of Xi'an Jiaotong University have conducted a study to assess the correlation between gut microbiota and ovarian responses to controlled ovarian stimulation. The study included 22 IVF cycles with a low follicle-to-oocyte index (FOI) and 25 IVF cycles with a higher FOI. The results showed that an increased abundance of certain gut bacteria, such as Prevotella copri and Bacteroides vulgatus, was associated with poor ovarian responsiveness, while an increased abundance of Bifidobacterium longum was associated with improved ovarian response. The study suggests that the integration of Bifidobacterium longum may enhance ovarian response. [Extracted from the article]

A recent study conducted by researchers at the National Center of Infectious and Parasitic Diseases in Sofia, Bulgaria, examined the impact of a large Waste Water Treatment Plant (WWTP) on the Iskar River. The study focused on the bacterial community dynamics and resistance profiles of the surface water downstream of the WWTP. The researchers found that antimicrobial resistance genes (ARGs) persisted in the water post-treatment, potentially spreading from human populated areas into the environment. The study highlights the need for continued monitoring of ARGs in freshwater systems. [Extracted from the article]

Researchers at the Telethon Kids Institute in Perth, Australia have conducted a study on the complexity of the human respiratory virome. The study aimed to explore the diversity of viruses in the respiratory tract and their potential impact on respiratory diseases. By analyzing shotgun metagenomic data retrieved from public repositories, the researchers identified viral contigs from 194 out of 868 processed files. These contigs represented a variety of viral genomes, including bacteriophages and previously uncharacterized viral genomes. The study provides new insights into viral communities in the respiratory tract and their potential influence on respiratory health. Further research is needed to validate these findings and understand the impact of these viral communities on respiratory physiology. [Extracted from the article]

Researchers at the Indian Institute for Technology in Delhi, India have reported new data on gene libraries. They prepared metagenomic fosmid libraries from soil and water samples collected from various locations and used them to screen and isolate D-amidase producers. The researchers found that the maximum number of libraries were obtained from soil rich in fishery waste, while the minimum number were obtained from tap water. They isolated a novel enzyme that showed catalytic promiscuity with various amides and had acyl transferase activity. The research has been peer-reviewed and published in Applied Biochemistry and Microbiology. [Extracted from the article]

A new study conducted by researchers at Panzhihua Central Hospital has identified a coinfection of Cedecea lapagei and Aspergillus sydowii in the bronchoalveolar lavage fluid of a patient with pulmonary infection. The study highlights the clinical significance of C. lapagei and the challenges in diagnosing A. sydowii. The researchers used metagenomic next-generation sequencing (mNGS) to accurately identify the pathogens. The findings emphasize the importance of precise identification of pathogens and the value of mNGS in detecting coinfections. [Extracted from the article]

This article discusses a study that analyzed the fecal microbiota of the critically endangered Eastern Bongo, a mammal known to have a sensitive gastrointestinal tract. The study used a metagenomic approach to examine the microbiota of two adult Eastern Bongos and six juvenile Bongos over a six-week period. The dominant phylum found in the samples was Bacillota, with Pseudomonadota dominant in only one of the juvenile samples. The study also examined functional classifications and resistomes. It is important to note that this preprint has not yet undergone peer review. [Extracted from the article]

Researchers from the University of Plymouth have conducted a study on the microbial diversity of the Roman Baths in Bath, UK, with the aim of discovering novel antimicrobial natural products (NPs) to combat antimicrobial resistance. Samples of water, biofilm, and sediment were collected and analyzed using metagenomic sequencing. The study found a shift in the dominant microbial communities between the King's Spring and the Great Bath, with bacteria being dominant in the latter. The researchers also isolated 15 isolates with broad-spectrum antimicrobial activity. This study highlights the potential for novel NP discovery from the Roman Baths. [Extracted from the article]

A new report discusses research findings on microorganism research conducted by a researcher at the University of Hong Kong. The study aimed to compare the metagenomic composition of saliva in denture wearers with different periodontal statuses. The research found that denture wearers are at an increased risk of developing periodontal diseases due to biofilm deposition and microbial colonization on the denture surface. The study also detected the presence of certain opportunistic pathogens in the microbial community of denture wearers. [Extracted from the article]

A recent report from Aarhus University in Roskilde, Denmark discusses the use of metagenomics to explore the genetic potential of microbial communities in extreme environments. The researchers focused on a metagenome from the cold and alkaline ikaite columns in Greenland and identified several putative carbohydrate-modifying enzymes with potential applications in detergents and other processes requiring low temperature and high pH. They synthesized and expressed selected enzymes in two host organisms, Escherichia coli and Aliivibrio wodanis, and found that Aliivibrio wodanis expressed a more diverse range of enzyme classes. One of the enzymes, Cel240, showed activity at low temperatures and good stability at 25 degrees C, making it a promising candidate for detergent and washing industry applications. [Extracted from the article]

A recent study conducted at Johns Hopkins University School of Medicine aimed to investigate the presence of pathogenic microorganisms in the corneal epithelial layer of keratoconus patients. The study used metagenomic next-generation sequencing to analyze corneal epithelial samples from both keratoconus patients and healthy controls. The results showed a low microbial read count in both groups, with no statistically significant difference between them. The study concluded that there is no evidence to support the hypothesis that chronic corneal infection is involved in the development of keratoconus, although it does not rule out the possibility of an acute infection as an initiating event. [Extracted from the article]

A recent report from Southern Medical University discusses the relationship between gut microbiota and acute lymphoblastic leukemia (ALL) in children undergoing chemotherapy. The study found that the composition and diversity of gut microbiota changed significantly during chemotherapy, with certain species such as Escherichia coli, Klebsiella pneumoniae, and Bifidobacterium longum being particularly prominent. The researchers also identified specific microbial metabolic pathways that were altered during chemotherapy. Additionally, the study found that the baseline gut microbiota could potentially serve as biomarkers for predicting infectious complications during chemotherapy. This research provides new insights into the acute changes in gut microbiota during ALL treatment and highlights the potential for using gut microbiota as predictive biomarkers. [Extracted from the article]

The article discusses biological studies into the holobiont concept which involves the genome of organisms. Topics explored include the application of metagenomics by researcher Thomas Bell and colleagues in analyzing the organelles of insects, amphibians, and plants, observations on the behavior of the resulting alliances between plants and microbes in the soil, and the involvement of the immune system in the interaction between host and microbiome.

A recent study conducted at Cotton University in Assam, India, has found that earthworms play a crucial role in the degradation of pollutants in the region's paddy fields. The study focused on the sequestration potential of lead (Pb) tolerant bacteria found in the gut of the earthworm species Metaphire nanaoensis. Four bacterial strains were identified as having the highest tolerance to lead, with Pseudomonas aeruginosa showing the maximum sequestration of Pb. The research highlights the importance of earthworms and their gut bacteria in bioremediation efforts and provides insights into microbial alterations that aid in the degradation of environmental pollutants. [Extracted from the article]

A study conducted at Xiangya Hospital in Changsha, China, has found that metagenomic next-generation sequencing (mNGS) may be more effective than procalcitonin and blood culture in diagnosing infectious pancreatic necrosis (IPN) in patients with febrile acute necrotizing pancreatitis (ANP). The study enrolled 78 patients with febrile ANP, of which 38.5% were confirmed to have IPN. mNGS showed a significantly higher sensitivity rate and outperformed procalcitonin and blood culture in terms of negative predictive value. The study suggests that blood mNGS could be an important tool in guiding antibiotic usage for patients with febrile ANP. [Extracted from the article]

A recent report from Microsoft Research discusses a metagenomic analysis of the Anopheles gambiae 1000 genomes dataset, which focuses on the genetic diversity of African An. gambiae populations. The study utilized deep sequencing methods and found evidence of various cobionts associated with field-collected mosquitoes, including vertebrate hosts, Plasmodium falciparum reads, human hepatitis B, and primate erythroparvovirus-1 viral sequences. The researchers also identified bacterial reads and bacteriophage-related contigs in some specimens. This analysis highlights the potential of metagenomic approaches in understanding vector-host-pathogen interactions. For more information, the full article can be accessed through Communications Biology. [Extracted from the article]

A recent study conducted in Shanghai, China, investigated the distribution of Mycobacterium in aerosol samples collected from metro environments. The study found that a total of 90 species of Mycobacterium were detected, with Mycobacterium tuberculosis being the most prevalent. The distribution of Mycobacterium was found to be related to factors such as season, temperature, and concentrations of CO2 and particulate matter. The researchers recommended implementing measures to control these factors in order to minimize the risk of Mycobacterium contamination in metro systems. [Extracted from the article]

A recent study conducted by investigators at the Faculty of Human Ecology in Bogor, Indonesia, explored the potential of using Telang flower (Clitoria Ternatea L.) to produce kombucha, a fermented tea beverage. The researchers conducted metagenomic analysis to examine the microbial ecology of the kombucha and assessed its safety aspects, including microbiological safety, organic acid content, heavy metal contamination, pH, and alcohol content. The study found that Telang flower kombucha is safe to consume, with no pathogenic bacteria or heavy metal contaminants detected. The fermentation process also increased the antioxidant compounds and activity in the beverage. This research provides valuable insights into the potential of Telang flower kombucha as an alternative functional beverage for health. [Extracted from the article]

Researchers from the Technical University of Denmark (DTU) have conducted a study on Listeria monocytogenes, a pathogen commonly transmitted through contaminated ready-to-eat food. The researchers used a novel metagenomic approach to identify genes associated with disinfectant tolerance in mixed L. monocytogenes planktonic communities. The study found that the abundance of Listeria phage-associated genes increased after treatment with disinfectants, suggesting that prophage carriage could lead to increased disinfectant tolerance. The researchers concluded that this metagenomic approach could be applied to identify genes associated with increased tolerance to other antimicrobials in mixed bacterial communities. [Extracted from the article]

A recent study conducted by researchers at the Centre de recherche du Centre hospitalier de l'Universite de Montreal (CRCHUM) explored the association between cancer cachexia (CC) and gut microbiome composition in patients with non-small cell lung cancer (NSCLC). The study collected fecal samples from 139 NSCLC patients and analyzed the gut microbiome using metagenomic techniques. The results showed that patients with CC had shorter progression-free survival and overall survival compared to those without CC. Additionally, the study identified distinct differences in the gut microbiome composition and metabolic potentials between the two groups. The findings suggest that gut microbiome profiling could serve as a novel screening method for CC. [Extracted from the article]

A recent study conducted by researchers at Hong Kong Polytechnic University has revealed high levels of contamination of pathogenic bacteria and antibiotic resistance genes (ARGs) in shrimp sold in markets and supermarkets. The study utilized metagenomic analysis and bacterial isolation to examine the microbial composition, ARGs, and virulence factors present in shrimp samples. The results showed a dominance of Proteobacteria and Bacteroidetes, with Firmicutes enriched in some samples. The study highlights the need for ongoing surveillance and intervention strategies to mitigate the risks posed by antibiotic-resistant bacteria in the food supply chain. [Extracted from the article]